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Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins

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Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins Supporting Information Out of the abyss: Genome and metagenome mining reveals unexpected environmental distribution of abyssomicins Alba Iglesias1, Adriel Latorre‐Pérez2, James E. M. Stach3, Manuel Porcar2,4, Javier Pascual2 1 School of Biology, Devonshire Building, Newcastle University, Newcastle, United Kingdom. 2 Darwin Bioprospecting Excellence SL, Paterna, Spain. 3 School of Biology, Ridley Building, Newcastle University, Newcastle, United Kingdom; Centre for Synthetic Biology and the Bioeconomy, Baddiley-Clark Building, Newcastle University, Newcastle, United Kingdom. 4 Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain. Corresponding author: [email protected] Contents Page Figure S1. Habitat distribution of the metagenomes analysed for the presence of AbyU, AbmU and AbsU. 2 Figure S2. Taxonomic profile at the phylum level of ten marine (1-10), ten terrestrial (11-20) and ten Diels- Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one 3 Arthropoda-associated (27) and three plant-associated (28-30). Only the most abundant phyla are shown. Numbers above each bar plot indicate metagenome size (Mb). Figure S3. Taxonomic profile at the order level of ten marine (1-10), ten terrestrial (11-20) and ten Diels- Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 4 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one Arthropoda-associated (27) and three plant-associated (28-30). Figure S4. Habitat distribution of the Diels-Alderase positive isolates found by genome mining. 5 Figure S5. Habitat distribution of the Diels-Alderase positive isolates found by genome mining to have an 6 abyssomicin or potential abyssomicin BGC (both total and partial). Figure S6. Habitat distribution of the Diels-Alderase positive isolates found by genome mining that do not 7 harbour any abyssomicin nor potential abyssomicin BGC. Figure S7. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters 8 type 1a and 1b. Figure S8. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters 9 type 2a and 2b. Figure S9. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters 10 type 3 and 4. Figure S10. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters 11 type 5. Figure S11. Potential tetronomycin BGC in S. olindensis, potential chlorothricin BGC from A. wychmicini and A. 12 pelletieri and quartromycin BGCs from A. albispora and A. orientalis. Table S1. Abyssomicin producing bacteria as reported in literature. 13 Table S2. Isolation details of the abyssomicin producers isolated from aquatic environments. 14 Table S3. Nucleotide and protein sequences of the Diels Alderase proteins present in aby, abs and abm 15 BGCs. Table S4. Identity percentage at protein (above) and nucleotide (below) level between the Diels Alderase 16 proteins present in aby, abs and abm BGCs. Table S5. Classification of metagenomic samples from aquatic environments mined for AbyU, AbsU and 17 AbmU. Numbers represent Diels-Alderase positive/mined metagenomes. Table S6. Classification of metagenomic samples from terrestrial environments mined for AbyU, AbsU and 18 AbmU. Numbers represent Diels-Alderase positive/mined metagenomes. Table S7. Classification of metagenomic samples from engineered environments mined for AbyU, AbsU and 19 AbmU. Numbers represent Diels-Alderase positive/mined metagenomes. Table S8. Classification of metagenomic samples from host-associated environments mined for AbyU, AbsU 20-21 and AbmU. Numbers represent Diels-Alderase positive/mined metagenomes. Table S9. Proteins within the non-redundant sequence database (NCBI) with significative alignments to AbyU, AbmU, AbsU and VASRM7_509. Columns displaying the Diels-Alderase homologs show 22-25 protein ID, alignment E-value and similarity percentage. Table S10. The abyssomicin biosynthetic gene cluster from M. maris AB-16-032 (modified from Gottardi et al., 26 2011). Table S11. The abyssomicin biosynthetic gene cluster from S. koyangensis SCSIO 5802 (modified from Song 27-28 et al., 2017). Table S12. The abyssomicin biosynthetic gene cluster from Streptomyces sp. LC-6-2 (adapted from Wang et 29-30 al., 2017). Table S13. The abyssomicin biosynthetic gene cluster from Verrucosispora sp. MS100047 (KF826681.1). 31 Table S14-S84. Recovered BGCs and ORFs surrounding AbyU homologs. 32-140 Table S85-S100. Predicted genomic islands. 141-171 References 172 1 Figure S1. Habitat distribution of the metagenomes analysed for the presence of AbyU, AbmU and AbsU. 2 Figure S2. Taxonomic profile at the phylum level of ten marine (1-10), ten terrestrial (11-20) and ten Diels-Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one Arthropoda-associated (27) and three plant-associated (28-30). Only the most abundant phyla are shown. Numbers above each bar plot indicate metagenome size (Mb). 3 Figure S3. Taxonomic profile at the order level of ten marine (1-10), ten terrestrial (11-20) and ten Diels-Alderase positive (21-30) metagenomes. These metagenomes were randomly selected from the 3027 metagenomes analysed. The ten Diels-Alderase positive were six terrestrial (21-26), one Arthropoda-associated (27) and three plant-associated (28-30). 4 Figure S4. Habitat distribution of the Diels-Alderase positive isolates found by genome mining. 5 Figure S5. Habitat distribution of the Diels-Alderase positive isolates found by genome mining to have an abyssomicin or potential abyssomicin BGC (both total and partial). 6 Figure S6. Habitat distribution of the Diels-Alderase positive isolates found by genome mining that do not harbour any abyssomicin nor potential abyssomicin BGC. 7 Figure S7. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters type 1a and 1b. Gene names in black are common to aby, abs and abm BGCs. Blue font represents genes present only in M. maris AB-18-032, grey font represents genes present only in Streptomyces sp. LC-6-2 and light blue font represent genes unique to S. koyangensis SCSIO 5802. In maroon font appear those genes that appear both in aby and abs BGCs, in light brown those genes that appear both in aby and abm BGCs and in yellow those genes that appear both in abs and abm BGCs. Grey boxes indicate the conserved regions shared between the type 1 clusters. Dotted lines indicate genetic islands. 8 Figure S8. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters type 2a and 2b. Gene names in black are common to aby, abs and abm BGCs. Blue font represents genes present only in M. maris AB-18-032, grey font represents genes present only in Streptomyces sp. LC-6-2 and light blue font represent genes unique to S. koyangensis SCSIO 5802. In maroon font appear those genes that appear both in aby and abs BGCs, in light brown those genes that appear both in aby and abm BGCs and in yellow those genes that appear both in abs and abm BGCs. Grey boxes indicate the conserved regions shared between the type 2 clusters. Dotted lines indicate genetic islands. 9 Figure S9. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters type 3 and 4. Gene names in black are common to aby, abs and abm BGCs. Gene names in black are common to aby, abs and abm BGCs. Blue font represents genes present only in M. maris AB-18-032, grey font represents genes present only in Streptomyces sp. LC-6-2 and light blue font represent genes unique to S. koyangensis SCSIO 5802. In maroon font appear those genes that appear both in aby and abs BGCs, in light brown those genes that appear both in aby and abm BGCs and in yellow those genes that appear both in abs and abm BGCs. Grey boxes indicate the conserved regions shared between the type 3 and type 4 clusters. Dotted lines indicate genetic islands. 10 Figure S10. Abyssomicin and potential abyssomicin BGCs recovered from genome mining classified as clusters type 5. Gene names in black are common to aby, abs and abm BGCs. Blue font represents genes present only in M. maris AB-18-032, grey font represents genes present only in Streptomyces sp. LC-6-2 and light blue font represent genes unique to S. koyangensis SCSIO 5802. In maroon font appear those genes that appear both in aby and abs BGCs, in light brown those genes that appear both in aby and abm BGCs and in yellow those genes that appear both in abs and abm BGCs. 11 Figure S11. Potential tetronomycin BGC in S. olindensis DAUFPE 5622, potential chlorothricin BGC from A. wychmicini DSM 45934 and A. pelletieri DSM 43383 and quartromycin BGCs from A. albispora WP1 and A. orientalis Q427-8. The Diels-Alderase homologs are displayed in blue. Dotted lines indicate genetic islands. 12 Table S1. Abyssomicin producing bacteria as reported in literature. Microorganism Isolation location Habitat Reference Accession Abyssomicin structure Sediment Sea of Japan Micromonospora maris AB-18-032 Aquatic (Riedlinger et al., 2004) JF752342 B, C, atrop-C, D, G, H (-289 m) Soil Ile de Paradis Streptomyces sp. HKI0381 Terrestrial (Niu et al., 2007) - E (Senegal) Rock soil Campeche Streptomyces sp. CHI39 Terrestrial (Igarashi
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